HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening

Abstract

BackgroundHigh-content screening (HCS) has become a powerful tool for drug discovery. However, the discovery of drugs targeting neurons is still hampered by the inability to accurately identify and quantify the phenotypic changes of multiple neurons in a single image (named multi-neuron image) of a high-content screen. Therefore, it is desirable to develop an automated image analysis method for analyzing multi-neuron images.ResultsWe propose an automated analysis method with novel descriptors of neuromorphology features for analyzing HCS-based multi-neuron images, called HCS-neurons. To observe multiple phenotypic changes of neurons, we propose two kinds of descriptors which are neuron feature descriptor (NFD) of 13 neuromorphology features, e.g., neurite length, and generic feature descriptors (GFDs), e.g., Haralick texture. HCS-neurons can 1) automatically extract all quantitative phenotype features in both NFD and GFDs, 2) identify statistically significant phenotypic changes upon drug treatments using ANOVA and regression analysis, and 3) generate an accurate classifier to group neurons treated by different drug concentrations using support vector machine and an intelligent feature selection method. To evaluate HCS-neurons, we treated P19 neurons with nocodazole (a microtubule depolymerizing drug which has been shown to impair neurite development) at six concentrations ranging from 0 to 1000 ng/mL. The experimental results show that all the 13 features of NFD have statistically significant difference with respect to changes in various levels of nocodazole drug concentrations (NDC) and the phenotypic changes of neurites were consistent to the known effect of nocodazole in promoting neurite retraction. Three identified features, total neurite length, average neurite length, and average neurite area were able to achieve an independent test accuracy of 90.28% for the six-dosage classification problem. This NFD module and neuron image datasets are provided as a freely downloadable MatLab project at http://iclab.life.nctu.edu.tw/HCS-Neurons.ConclusionsFew automatic methods focus on analyzing multi-neuron images collected from HCS used in drug discovery. We provided an automatic HCS-based method for generating accurate classifiers to classify neurons based on their phenotypic changes upon drug treatments. The proposed HCS-neurons method is helpful in identifying and classifying chemical or biological molecules that alter the morphology of a group of neurons in HCS.

Histone acetylation inhibitors promote axon growth in adult dorsal root ganglia neurons

“…To test the effect of microtubule‐stabilizing and ‐destabilizing drugs, taxol (10 nM) and nocodazole (300 nM) were applied to cultured DRG neurons. These concentrations were chosen from results observed by others in cultured neurons in vitro (Sengottuvel and Fischer, ; Charoenkwan et al, ). Measurement of the longest axon lengths and total axon lengths of each neuron showed no significant difference between taxol (mean total length 1,301.7 ± 232.1 μm, mean longest length 469.3 ± 40.2 μm) and control DMSO treatments (mean total length 1,135.3 ± 125.5 μm, mean longest length 422.8 ± 42.5 μm).…”

In vitro acute and developmental neurotoxicity screening: an overview of cellular platforms and high-throughput technical possibilities

“…For neurocytotoxicity HCI testing of compound libraries containing several thousand compounds on several cell types/lines in parallel, the expected image numbers will be extremely high (up to billions), and automated data processing pipelines are mandatory to handle the amounts of information more efficiently. A number of automated image analysis tools have been developed to process images and to analyse features of neurocytotoxicity [see (Billeci et al 2013) for an overview of tools], we would mention NeurphologyJ (an ImageJ plugin), HCS-Neurons, NEMO, and Cellprofiler here (Carpenter et al 2006;Ho et al 2011;Billeci et al 2013;Charoenkwan et al 2013;Dreser et al 2015). HCS-Neurons aim at analysing the groups of neurons (multineuron images), and NEMO provides the user with a unique function enabling the analysis of sequences of time-lapse images.…”

Rat embryonic hippocampus and induced pluripotent stem cell derived cultured neurons recover from laser-induced subaxotomy

“…Experiments using fluorescent dyes or forster resonance energy transfer-based biosensors will be useful in the elucidation of the intracellular signaling pathways involved in sensing and repair of axonal damage. 32 In addition, several inhibitors, such as cytochalasin D, 33 Nocodazole, 34 and ROCK, 35 will be used in future studies involving cytoskeletal remodeling following laser subaxotomy. In conclusion, laser subaxotomy at the single-cell level can contribute to an understanding of the repair mechanism necessary to restore damaged neuronal circuits at the tissue and organ levels.…”